Variant report

Variant	rs1859462
Chromosome Location	chr14:71282607-71282608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71282463..71285169-chr14:71374308..71376107,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCNX-2	chr14:71281828-71283587	NONHSAT037592

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12590049	0.88[EUR][1000 genomes]
rs17108554	0.81[EUR][1000 genomes]
rs17177097	0.88[EUR][1000 genomes]
rs17177187	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17766621	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859463	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902856	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61990520	0.81[EUR][1000 genomes]
rs61990551	0.82[AMR][1000 genomes]
rs6573983	0.82[AMR][1000 genomes]
rs7141204	0.82[AMR][1000 genomes]
rs7153836	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8018972	0.81[EUR][1000 genomes]
rs8019053	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8020803	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71277200-71288000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr14:71277200-71288400	Weak transcription	Pancreas	Pancrea
3	chr14:71277400-71283800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:71277800-71284200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr14:71277800-71288000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr14:71278000-71283800	Weak transcription	Brain Hippocampus Middle	brain
7	chr14:71278000-71284200	Weak transcription	Hela-S3	cervix
8	chr14:71278200-71284200	Weak transcription	Dnd41	blood
9	chr14:71278400-71284000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr14:71279000-71283200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr14:71279200-71283000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:71279200-71283200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:71279200-71283400	Weak transcription	A549	lung
14	chr14:71279400-71283200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr14:71279400-71283800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:71279400-71286200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:71279400-71288000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:71279600-71283200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr14:71279600-71283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr14:71279600-71283200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr14:71279600-71283400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr14:71279600-71283400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr14:71279600-71284200	Weak transcription	Brain Anterior Caudate	brain
24	chr14:71279800-71283800	Weak transcription	HepG2	liver
25	chr14:71280000-71283200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr14:71280200-71284000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr14:71280200-71287800	Weak transcription	NHEK	skin
28	chr14:71280600-71284200	Weak transcription	Fetal Brain Female	brain
29	chr14:71281400-71284000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr14:71281400-71284400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr14:71282000-71282800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr14:71282000-71284000	Weak transcription	GM12878-XiMat	blood
33	chr14:71282000-71284200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr14:71282000-71284400	Weak transcription	Fetal Brain Male	brain
35	chr14:71282400-71283800	Weak transcription	Fetal Heart	heart
36	chr14:71282600-71283800	Weak transcription	HMEC	breast

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